Wither isn't Nasus's ultimate, which makes it pretty easy to use around an ult-level CD QSS active.
Wither has a pretty non-existent cooldown, so short of running directly at Vayne by yourself like a derp, Nasus can deal with that. Bait the QSS, use brush, approach Vayne from an angle you'll hit her without her being slowed in the first place, run back a bit so Vayne hyper-accelerates into your back then turn around to whack her as sort of a fient...
Wither isn't exactly necessary for Nasus to do things, especially if he's played by someone smarter than your average bear.
Also - item counters are available to every champion and cost gold, which pretty much invalidates your point here. Nasus can just as easily get items that make Vayne's job significantly harder.
Nasus can get "more" items than Vayne to do that in this case as well, seeing as the OP is complaining about a different item than Mercurial Scimitar.
And an average game only lasts ~33 minutes and sees almost exactly ~11,000 gold per player.
Which is 3 major ~3k items, ~1k in boots, and ~1k in the bank after the final team fight when someone's Nexus explodes.
The last major item likely isn't going to be complete for it's unique effects until said final team fight as well, which makes the first 2 major core items rather important.
A significant portion of the game time is going to pass between the acquisition of each major item, a significant portion of the game is Vayne simply not having those items.